Masaryk University

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    2024

    1. AlphaFind: Discover structure similarity across the entire known proteome
      PROCHÁZKA, David, Terézia SLANINÁKOVÁ, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ, Miriama JÁNOŠOVÁ, Jakub ČILLÍK, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL and Matej ANTOL. AlphaFind: Discover structure similarity across the entire known proteome. bioRxiv, 2024.
      AlphaFind web application Pre-print
      Czech Republic.
      Keywords in English: Protein structure similarity;Learned metric index;Learned indexing;Protein structure search;AlphaFold DB
      International impact: yes
      Changed by: RNDr. Terézia Slanináková, učo 445526. Changed: 19/2/2024 10:17.
      More: https://is.muni.cz/publication/2375820/en

    2023

    1. Reproducible experiments with Learned Metric Index Framework
      SLANINÁKOVÁ, Terézia, Matej ANTOL, Jaroslav OĽHA, Vlastislav DOHNAL, Susana LADRA and Miguel A. MARTÍNEZ-PRIETO. Reproducible experiments with Learned Metric Index Framework. Information systems. Elsevier, 2023, vol. 118, No 1, p. 102255-102270. ISSN 0306-4379. Available from: https://dx.doi.org/10.1016/j.is.2023.102255.
      URL
      RIV/00216224:14330/23:00131386 Article in a journal. English. Netherlands.
      Slanináková, Terézia (703 Slovakia, belonging to the institution) -- Antol, Matej (703 Slovakia, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Dohnal, Vlastislav (203 Czech Republic, guarantor, belonging to the institution) -- Ladra, Susana (724 Spain) -- Martínez-Prieto, Miguel A. (724 Spain)
      Keywords in English: Reproducible paper;Index structures;Learned index;Unstructured data;Content-based search;Metric space
      International impact: yes
      Reviewed: yes
      Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 7/4/2024 23:08.
      More: https://is.muni.cz/publication/2301611/en
    2. SISAP 2023 Indexing Challenge – Learned Metric Index
      SLANINÁKOVÁ, Terézia, David PROCHÁZKA, Matej ANTOL, Jaroslav OĽHA and Vlastislav DOHNAL. SISAP 2023 Indexing Challenge – Learned Metric Index. In Pedreira, O., Estivill-Castro, V. Similarity Search and Applications. SISAP 2023. Lecture Notes in Computer Science, vol 14289. Cham: Springer, 2023, p. 282-290. ISBN 978-3-031-46993-0. Available from: https://dx.doi.org/10.1007/978-3-031-46994-7_24.
      RIV/00216224:14330/23:00132045 Proceedings paper. English. Switzerland.
      Slanináková, Terézia (703 Slovakia, belonging to the institution) -- Procházka, David (203 Czech Republic, belonging to the institution) -- Antol, Matej (703 Slovakia, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Dohnal, Vlastislav (203 Czech Republic, guarantor, belonging to the institution)
      Keywords in English: sisap indexing challenge; learned metric index; similarity search; machine learning for indexing; performance benchmarking
      Type of proceedings: post-proceedings
      International impact: yes
      Reviewed: yes
      Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 7/4/2024 23:35.
      More: https://is.muni.cz/publication/2330525/en
    3. Umpalumpa: a framework for efficient execution of complex image processing workloads on heterogeneous nodes
      STŘELÁK, David, David MYŠKA, Filip PETROVIČ, Jan POLÁK, Jaroslav OĽHA and Jiří FILIPOVIČ. Umpalumpa: a framework for efficient execution of complex image processing workloads on heterogeneous nodes. Computing. Springer, 2023, vol. 105, No 11, p. 2389-2417. ISSN 0010-485X. Available from: https://dx.doi.org/10.1007/s00607-023-01190-w.
      URL
      RIV/00216224:14610/23:00131054 Article in a journal. English. Austria.
      Střelák, David (203 Czech Republic, belonging to the institution) -- Myška, David (203 Czech Republic, belonging to the institution) -- Petrovič, Filip (703 Slovakia, belonging to the institution) -- Polák, Jan (203 Czech Republic, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Filipovič, Jiří (203 Czech Republic, belonging to the institution)
      Keywords in English: Image processing; task-based systems; auto-tuning; data-aware architecture; CUDA
      International impact: yes
      Reviewed: yes
      Changed by: RNDr. Jiří Filipovič, Ph.D., učo 72898. Changed: 21/3/2024 08:53.
      More: https://is.muni.cz/publication/2293221/en

    2022

    1. Learned Indexing in Proteins: Extended Work on Substituting Complex Distance Calculations with Embedding and Clustering Techniques
      OĽHA, Jaroslav, Terézia SLANINÁKOVÁ, Martin GENDIAR, Matej ANTOL and Vlastislav DOHNAL. Learned Indexing in Proteins: Extended Work on Substituting Complex Distance Calculations with Embedding and Clustering Techniques. arXiv, 2022. Available from: https://dx.doi.org/10.48550/ARXIV.2208.08910.
      URL
      Name (in English): Learned Indexing in Proteins: Extended Work on Substituting Complex Distance Calculations with Embedding and Clustering Techniques
      English. United States of America.
      Keywords in English: Protein database;Embedding non-vector data;Learned metric index;Similarity search;Machine learning for indexing
      International impact: yes
      Changed by: Mgr. et Mgr. Jaroslav Oľha, učo 348646. Changed: 10/1/2023 07:51.
      More: https://is.muni.cz/publication/2212035/en
    2. Learned Indexing in Proteins: Substituting Complex Distance Calculations with Embedding and Clustering Techniques
      OĽHA, Jaroslav, Terézia SLANINÁKOVÁ, Martin GENDIAR, Matej ANTOL and Vlastislav DOHNAL. Learned Indexing in Proteins: Substituting Complex Distance Calculations with Embedding and Clustering Techniques. In Tomáš Skopal, Fabrizio Falchi, Jakub Lokoč, Maria Luisa Sapino, Ilaria Bartolini, Marco Patella. Similarity Search and Applications, 15th International Conference, SISAP 2022, Bologna, Italy, October 5–7, 2022, Proceedings. 1st ed. Cham: Springer Cham, 2022, p. 274-282. ISBN 978-3-031-17848-1. Available from: https://dx.doi.org/10.1007/978-3-031-17849-8_22.
      URL
      Name (in English): Learned Indexing in Proteins: Substituting Complex Distance Calculations with Embedding and Clustering Techniques
      RIV/00216224:14330/22:00126460 Proceedings paper. English. Switzerland.
      Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Slanináková, Terézia (703 Slovakia, belonging to the institution) -- Gendiar, Martin (703 Slovakia, belonging to the institution) -- Antol, Matej (703 Slovakia, belonging to the institution) -- Dohnal, Vlastislav (203 Czech Republic, guarantor, belonging to the institution)
      Keywords in English: Protein database;Embedding non-vector data;Learned metric index;Similarity search;Machine learning for indexing
      Type of proceedings: post-proceedings
      International impact: yes
      Reviewed: yes
      Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 16/8/2023 13:25.
      More: https://is.muni.cz/publication/2212037/en
    3. Property Map Collective Variable as a Useful Tool for a Force Field Correction
      TRAPL, Dalibor, MArtin KRUPIČKA, Vladimír VIŠŇOVSKÝ, Jana HOZZOVÁ, Jaroslav OĽHA, Aleš KŘENEK and Vojtěch SPIWOK. Property Map Collective Variable as a Useful Tool for a Force Field Correction. Journal of Chemical Information and Modeling. American Chemical Society, 2022, vol. 62, No 3, p. 567-576. ISSN 1549-9596. Available from: https://dx.doi.org/10.1021/acs.jcim.1c00651.
      URL
      Name in Czech: Property Map Collective Variable as a Useful Tool for a Force Field Correction
      Name (in English): Property Map Collective Variable as a Useful Tool for a Force Field Correction
      RIV/00216224:14610/22:00129035 Article in a journal. English. United States of America.
      Trapl, Dalibor (203 Czech Republic) -- Krupička, MArtin (203 Czech Republic) -- Višňovský, Vladimír (703 Slovakia, belonging to the institution) -- Hozzová, Jana (703 Slovakia, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Křenek, Aleš (203 Czech Republic, guarantor, belonging to the institution) -- Spiwok, Vojtěch (203 Czech Republic)
      Keywords in English: collective variable; biased potential; force field
      International impact: yes
      Reviewed: yes
      Changed by: Mgr. Alena Mokrá, učo 362754. Changed: 14/3/2023 15:51.
      More: https://is.muni.cz/publication/1839946/en
    4. Using hardware performance counters to speed up autotuning convergence on GPUs
      FILIPOVIČ, Jiří, Jana HOZZOVÁ, Amin NEZARAT, Jaroslav OĽHA and Filip PETROVIČ. Using hardware performance counters to speed up autotuning convergence on GPUs. Journal of Parallel and Distributed Computing. Elsevier, 2022, vol. 160, February, p. 16-35. ISSN 0743-7315. Available from: https://dx.doi.org/10.1016/j.jpdc.2021.10.003.
      URL
      RIV/00216224:14610/22:00125022 Article in a journal. English. Netherlands.
      Filipovič, Jiří (203 Czech Republic, guarantor, belonging to the institution) -- Hozzová, Jana (703 Slovakia, belonging to the institution) -- Nezarat, Amin (364 Islamic Republic of Iran, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Petrovič, Filip (703 Slovakia, belonging to the institution)
      Keywords in English: Auto-tuning; Search method; Performance counters; CUDA
      International impact: yes
      Reviewed: yes
      Changed by: RNDr. Jiří Filipovič, Ph.D., učo 72898. Changed: 20/3/2023 12:40.
      More: https://is.muni.cz/publication/1799520/en

    2021

    1. Complex simulation workflows in containerized high-performance environment
      VIŠŇOVSKÝ, Vladimír, Viktória SPIŠAKOVÁ, Jana HOZZOVÁ, Jaroslav OĽHA, Dalibor TRAPL, Vojtěch SPIWOK, Lukáš HEJTMÁNEK and Aleš KŘENEK. Complex simulation workflows in containerized high-performance environment. In Armenia S., Geril P. Proc. ESM 2021. Brusel: EUROSIS, 2021, p. 42-45. ISBN 978-94-92859-18-1.
      Name (in English): Complex simulation workflows in containerized high-performance environment
      RIV/00216224:14610/21:00119698 Proceedings paper. English. Belgium.
      Višňovský, Vladimír (703 Slovakia, belonging to the institution) -- Spišaková, Viktória (703 Slovakia, belonging to the institution) -- Hozzová, Jana (703 Slovakia, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Trapl, Dalibor (203 Czech Republic) -- Spiwok, Vojtěch (203 Czech Republic) -- Hejtmánek, Lukáš (203 Czech Republic, belonging to the institution) -- Křenek, Aleš (203 Czech Republic, guarantor, belonging to the institution)
      Keywords in English: Docker; Jupyter notebook; Kubernetes; Molecular force field; Protein folding; Reproducibility; Workflow
      Type of proceedings: pre-proceedings
      International impact: yes
      Reviewed: yes
      Changed by: Mgr. Alena Mokrá, učo 362754. Changed: 30/3/2023 14:31.
      More: https://is.muni.cz/publication/1839944/en
    2. Data-driven Learned Metric Index: an Unsupervised Approach
      SLANINÁKOVÁ, Terézia, Matej ANTOL, Jaroslav OĽHA and Vlastislav DOHNAL. Data-driven Learned Metric Index: an Unsupervised Approach. In 14th International Conference on Similarity Search and Applications (SISAP 2021). Cham: Springer, 2021, p. 81-94. ISBN 978-3-030-89656-0. Available from: https://dx.doi.org/10.1007/978-3-030-89657-7_7.
      Name (in English): Data-driven Learned Metric Index: an Unsupervised Approach
      RIV/00216224:14330/21:00119191 Proceedings paper. English. Netherlands.
      Slanináková, Terézia (703 Slovakia, belonging to the institution) -- Antol, Matej (703 Slovakia, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Dohnal, Vlastislav (203 Czech Republic, guarantor, belonging to the institution)
      Keywords in English: Index structures; Learned index; Unstructured data; Content-based search; Metric space; Machine learning
      Type of proceedings: pre-proceedings
      International impact: yes
      Reviewed: yes
      Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 29/4/2022 08:12.
      More: https://is.muni.cz/publication/1790340/en
    3. Learned metric index - proposition of learned indexing for unstructured data
      ANTOL, Matej, Jaroslav OĽHA, Terézia SLANINÁKOVÁ and Vlastislav DOHNAL. Learned metric index - proposition of learned indexing for unstructured data. Information Systems. Elsevier, 2021, vol. 100, No 101774, p. 1-12. ISSN 0306-4379. Available from: https://dx.doi.org/10.1016/j.is.2021.101774.
      URL
      RIV/00216224:14330/21:00118915 Article in a journal. English. Netherlands.
      Antol, Matej (703 Slovakia, guarantor, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Slanináková, Terézia (703 Slovakia, belonging to the institution) -- Dohnal, Vlastislav (203 Czech Republic, belonging to the institution)
      Keywords in English: Index structures;Learned index;Unstructured data;Content-based search;Metric space
      International impact: yes
      Reviewed: yes
      Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 28/4/2022 09:52.
      More: https://is.muni.cz/publication/1757938/en
    4. Searching CUDA code autotuning spaces with hardware performance counters: data from benchmarks running on various GPU architectures
      HOZZOVÁ, Jana, Jiří FILIPOVIČ, Amin NEZARAT, Jaroslav OĽHA and Filip PETROVIČ. Searching CUDA code autotuning spaces with hardware performance counters: data from benchmarks running on various GPU architectures. Data in Brief. Elsevier, 2021, vol. 39, December, p. 1-12. ISSN 2352-3409. Available from: https://dx.doi.org/10.1016/j.dib.2021.107631.
      URL
      RIV/00216224:14610/21:00123013 Article in a journal. English. Netherlands.
      Hozzová, Jana (703 Slovakia, belonging to the institution) -- Filipovič, Jiří (203 Czech Republic, guarantor, belonging to the institution) -- Nezarat, Amin (364 Islamic Republic of Iran, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Petrovič, Filip (703 Slovakia, belonging to the institution)
      Keywords in English: Auto-tuning; Tuning spaces; Performance counters; CUDA
      International impact: yes
      Reviewed: yes
      Changed by: RNDr. Jiří Filipovič, Ph.D., učo 72898. Changed: 2/2/2022 14:05.
      More: https://is.muni.cz/publication/1805266/en

    2020

    1. A benchmark set of highly-efficient CUDA and OpenCL kernels and its dynamic autotuning with Kernel Tuning Toolkit
      PETROVIČ, Filip, David STŘELÁK, Jana HOZZOVÁ, Jaroslav OĽHA, Richard TREMBECKÝ, Siegfried BENKNER and Jiří FILIPOVIČ. A benchmark set of highly-efficient CUDA and OpenCL kernels and its dynamic autotuning with Kernel Tuning Toolkit. Future Generation Computer Systems. Elsevier, 2020, vol. 108, July, p. 161-177. ISSN 0167-739X. Available from: https://dx.doi.org/10.1016/j.future.2020.02.069.
      URL
      Name in Czech: Sada benchmarků vysoce efektivních CUDA a OpenCL kernelů a její dynamický autotuning za pomocí Kernel Tuning Toolkit
      RIV/00216224:14610/20:00115375 Article in a journal. English. Netherlands.
      Petrovič, Filip (703 Slovakia, belonging to the institution) -- Střelák, David (203 Czech Republic, belonging to the institution) -- Hozzová, Jana (703 Slovakia, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Trembecký, Richard (703 Slovakia, belonging to the institution) -- Benkner, Siegfried (40 Austria) -- Filipovič, Jiří (203 Czech Republic, guarantor, belonging to the institution)
      Keywords in English: Dynamic autotuning; OpenCL; CUDA; Performance optimization; Autotuning benchmark set
      International impact: yes
      Reviewed: yes
      Changed by: Mgr. Alena Mokrá, učo 362754. Changed: 25/3/2021 10:45.
      More: https://is.muni.cz/publication/1630456/en
    2. Exploiting historical data: Pruning autotuning spaces and estimating the number of tuning steps
      OĽHA, Jaroslav, Jana HOZZOVÁ, Jan FOUSEK and Jiří FILIPOVIČ. Exploiting historical data: Pruning autotuning spaces and estimating the number of tuning steps. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE. HOBOKEN: WILEY, 2020, vol. 32, No 21, p. 1-15. ISSN 1532-0626. Available from: https://dx.doi.org/10.1002/cpe.5962.
      URL
      RIV/00216224:14610/20:00116267 Article in a journal. English. United States of America.
      Oľha, Jaroslav (703 Slovakia, guarantor, belonging to the institution) -- Hozzová, Jana (703 Slovakia, belonging to the institution) -- Fousek, Jan (203 Czech Republic, belonging to the institution) -- Filipovič, Jiří (203 Czech Republic, belonging to the institution)
      Keywords in English: autotuning; prediction of tuning cost; sensitivity analysis; tuning space pruning
      International impact: yes
      Reviewed: yes
      Changed by: Mgr. Michal Petr, učo 65024. Changed: 30/8/2022 14:20.
      More: https://is.muni.cz/publication/1675386/en
    3. Exploring Protein Folding Space with Neural Network Guided Simulations
      KŘENEK, Aleš, Jana HOZZOVÁ, Jaroslav OĽHA, Dalibor TRAPL and Vojtěch SPIWOK. Exploring Protein Folding Space with Neural Network Guided Simulations. In Alexandre Nketsa. MODELLING AND SIMULATION 2020. Brusel: EUROSIS-ETI, 2020, p. 305-309. ISBN 978-94-92859-12-9.
      program konference
      Name in Czech: Prohledávání prostoru foldování proteinů simulacemí řízenými neuronovou sítí
      Name (in English): Exploring Protein Folding Space with Neural Network Guided Simulations
      RIV/00216224:14610/20:00114384 Proceedings paper. English. Belgium.
      Křenek, Aleš (203 Czech Republic, guarantor, belonging to the institution) -- Hozzová, Jana (703 Slovakia, belonging to the institution) -- Oľha, Jaroslav (703 Slovakia, belonging to the institution)
      Keywords in English: metadyamic; protein folding; netural network
      Type of proceedings: pre-proceedings
      International impact: yes
      Reviewed: yes
      Changed by: Mgr. Alena Mokrá, učo 362754. Changed: 29/4/2021 10:58.
      More: https://is.muni.cz/publication/1686702/en

    2019

    1. Exploiting historical data: pruning autotuning spaces and estimating the number of tuning steps
      OĽHA, Jaroslav, Jana HOZZOVÁ, Jan FOUSEK and Jiří FILIPOVIČ. Exploiting historical data: pruning autotuning spaces and estimating the number of tuning steps. In Ulrich Schwardmann, Christian Boehme, Dora B. Heras, Valeria Cardellini, Emmanuel Jeannot, Antonio Salis, Claudio Schifanella, Ravi Reddy Manumachu, Dieter Schwamborn, Laura Ricci, Oh Sangyoon, Thomas Gruber, Laura Antonelli, Stephen L. Scott. Lecture Notes in Computer Science. Cham, Switzerland: Springer, Cham, 2019, p. 295-307. ISBN 978-3-030-48339-5. Available from: https://dx.doi.org/10.1007/978-3-030-48340-1_23.
      Name in Czech: Využití historických dat: prořezávání prostorů v autotuningu a odhad počtu tunících kroků
      RIV/00216224:14610/19:00115100 Proceedings paper. English. Switzerland.
      Oľha, Jaroslav (703 Slovakia, belonging to the institution) -- Hozzová, Jana (703 Slovakia, belonging to the institution) -- Fousek, Jan (203 Czech Republic, belonging to the institution) -- Filipovič, Jiří (203 Czech Republic, guarantor, belonging to the institution)
      Keywords in English: Autotuning; prediction of tuning cost; tuning space pruning; sensitivity analysis
      Type of proceedings: post-proceedings
      International impact: yes
      Reviewed: yes
      Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 16/8/2023 15:53.
      More: https://is.muni.cz/publication/1551680/en

    2018

    1. Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations
      PAZÚRIKOVÁ, Jana, Jaroslav OĽHA, Aleš KŘENEK and Vojtěch SPIWOK. Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations. arXiv, 2018, 22 pp. arXiv:1801.02362.
      URL
      Name in Czech: Zrychlení výpočtů průměrných čtvercových vzdáleností s pohyblivou blízkou strukturou v metydynamických simulacích

      Keywords in English: approximation, acceleration, molecular dynamics simulation, metadynamics
      International impact: yes
      Changed by: Ing. Jana Hozzová, Ph.D., učo 411498. Changed: 28/1/2019 09:55.
      More: https://is.muni.cz/publication/1401896/en
Displayed: 3/5/2024 02:33